I actually didn't mind the boss fights that much, but that's probably because I don't really see the appeal in playing a non-lethal character, especially since there are no non-lethal sniper rifles in Deus Ex. Besides, all of them can be easily killed by either placing mines at their spawn point, bringing a turret or just spamming Typhoon, so it's not like you really have to fight them directly.
I guess my real problems with HR were the gameplay and the story.
While the gameplay worked very well, there was just barely any variety to keep things interesting for very long. There are just three different kinds of guards and if you're playing stealth there might as well be just one.
I'm not asking for the aliens or Half-Life rejects the original introduced (hell no), but how about melee focused enemies that can break your stupid one-hit-instant-kill attack? Enemies that can see through your cloak? Enemies that are immune to tranqs? See and shoot through walls?
By the middle of the game there were so many ways to completely break it: Enhanced vision + laser rifle, Typhoon spamming, the cloak; some enemies to counter that would have been nice.
The story was pretty good for the most part, but it really failed as a prequel.
If you preordered the game Jensen interacts with exactly one character from the original, the only character we learn anything new about is Manderley before he joined Unatco. That's it, really; like 3 other characters are also name dropped, but we learn nothing relevant except that they were indeed alive in 2027. We don't learn anything about Unatco's founding, nothing about DeBeer or the other Illuminati, nothing about anything that leads up to DE.
I had a few other issues, mostly in the story department, but those two problems are what made HR - while still a pretty good game - ultimately a disappointment for me. Phew, good thing this EP came up; since I'm fairly late to the party I didn't know where else to whine.